: Availability and affordability of essential medicines for chronic diseases in low- and middle-income countries both in the public and private sectors were considered low. This study aimed to evaluate medicines availability for non-communicable diseases (diabetes, hypertension, and cardiovascular disease), as well as to explore prices and the affordability of those drugs. Survey methodology was based on World Health Organization and Health Action International Manual (WHO/HAI). The survey was conducted in 24 health facilities randomly selected based on the representative for public and private health facilities. Chronic diseases including diabetes, hypertension, and cardiovascular disease, and twelve key medicines were identified and investigated. A high availability (>80%) of the medicines for diabetes was seen in the survey. Metformin had the highest availability among all medicines (100%). Captopril had the highest availability (87.50%) among hypertension medicines while propranolol had the lowest (66.67%). For cardiovascular medicines, a quite low availability (50-80%) was seen where simvastatin had the highest availability (62.50%) and Isosorbid dinitrate had the lowest (50%). The prices of 8 medicines were higher than IRP of the particular medicine. It means that the prices of theses medicines in most health facilities were expensive and not efficient. Less than ten day’s wages were required to buy a month’s supply of all medicines observed in this study. Over all availability of NCDs (diabetes, hypertension, and cardiovascular disease) medicines was suboptimal. Procurement price for most medicines surveyed was not efficient. All medicines surveyed are generally affordable to the lowest income community in the country. The relatively low availability and high MPR of NCDs medicines in health facilities of is a concern to make regulations to ensure availability and affordability of essential medicines in Indonesia. These policies are also important in the era of universal health coverage.